Several candidate risk genes and genomic regions for schizophrenia (SZ) have been identified as well as numerous environmental risk factors. The etiology of SZ, however, remains unknown. Some of the environmental influences may act through epigenetic mechanisms (e.g., DNA methylation and histone modifications) which can alter gene expression by influencing functional DNA elements (e.g., promoters or enhancers), thus altering transcription. Accumulating evidence suggests that epigenetic alterations are involved in the pathophysiology of SZ. A deficiency in gamma-amino butyric acid (GABA) neurotransmission in the prefrontal cortex (PFC) of affected individuals is one of the most consistent findings in SZ and has been reported in specimens from at least 10 different brain banks. This deficiency is present in a substantial proportion, but not all, individuals with SZ. We aim to explore the role of epigenetic alterations n this deficit. The GABAergic deficiency largely involves subpopulations of GABA interneurons that originate from the medial ganglionic eminence (MGE), and express the calcium-binding proteins par albumin (PVALB) or somatostatin (SST). The mechanisms that lead to the molecular pathology of these interneurons are incompletely understood but appear to involve altered expression of ontogenetic transcription factors [e.g., SRY (Sex Determining Region Y)-Box 6 (SOX6)], which play a critical role in the specification, migration, and maturation of the MGE-derived GABA interneurons. We speculate that in the subset of individuals with SZ who exhibit a prefrontal GABAergic deficit, the deficit is mediated in part through epigenetic anomalies involving the MGE-derived GABA interneurons. The proposed study in autopsy specimens is the first and necessary step in testing this epigenetic hypothesis. Specifically, we aim to characterize SZ-related differences in epigenetic marks in this particular cell population isolated from postmortem human brain. We have recently developed a fluorescence activated cell sorting (FACS)-based technique that provides excellent separation of neuronal (i.e., positive for the neuronal marker NeuN) nuclei from the postmortem brain into SOX6-positive and SOX6-negative subpopulations. The former population is highly enriched in PVALB- and SST-positive GABA interneurons, while the latter is mostly derived from glutamatergic (GLU) projection neurons. This methodological approach enables us to address epigenetic abnormalities in SZ that are specific for the MGE-derived GABA cells. Our first aim is to perform genome-wide chromatin profiling of GABA and GLU neurons in the PFC from psychiatrically normal control individuals using DNA methylation and histone modification marks indicative of functional DNA cis regulatory elements (CREs) (i.e., enhancers and promoters). Our second aim is to identify epigenetic alterations in the CREs of MGE-derived cortical GABA interneurons in individuals with SZ. We will validate the functional importance of our epigenetic findings by determining which genes that are epigenetically altered in SZ also exhibit altered transcription. The combination of technical innovation and multifaceted experimental design proposed in our work will advance fundamental neuroscience, and the resulting data will enhance our understanding of the cellular and molecular substrates of SZ. This may include the identification of epigenetic alterations that may be targeted in the future by novel therapeutic interventions. The proposed research may also provide important insights into the heterogeneity of molecular abnormalities underlying SZ which may correspond to the heterogeneity of clinical manifestations and therapeutic responses. This line of research, therefore, has the potential to contribute to enhanced personalized treatment selection in the future.